The functional state of enrichment cultures of the Eustigmatophycean strains Vischeria vischeri MZ–E3 and MZ–E4 after 25-day cultivation in the BBM medium was studied. The concentrations of chlorophyll a, total carotenoids, protein, vitamins A and E, fatty acid peroxidation product content, an antioxidant enzyme, and succinate dehydrogenase activity were measured. MZ–E3 succinate dehydrogenase activity was significantly higher by 2.21 times; the MZ–E4 strain had 2.94 times higher glutathione peroxidase activity. The MZ–E3 antioxidant activity index and the MZ–E3 unsaturation of fatty acids were 1.3 and 1.25 times higher than the MZ–E4. The retinol and α-tocopherol content of the MZ–E3 was 28.6% and 38.76% higher than MZ–E4. The main fatty acid profile differences were the 3.46-fold and 3.92-fold higher stearic and eicosapentaenoic acid content in the MZ–E4 biomass. MZ–E3 had higher antioxidant, energy, and metabolic and photosynthetic status than MZ–E4. The antioxidant status of the studied strains showed the dependence of the adaptive mechanisms of each, associated with differences in the ecological conditions of the biotopes from which they were isolated. These strains are promising for producing α-tocopherol and biomass enriched with omega-3 and omega-6 fatty acids.